featureSpectra() and chromPeakSpectra() to allow addition
of chromPeaks() and featuresDefinitions() columns to be added to the
Spectra output.xcms vignette, to order the filtering of features and remove
the outdated normalisation paragraph.In depth discussion on this subject can
be found on metabonaut.matchLamaChromPeaks() function to get the chromPeaksId
of the chromPeaks matched with Lamas.chromatogram() with msLevel = 2 fails to extract
chromatographic data if isolationWindowTargetMz is not specified or
available (e.g. for MSe data).XcmsExperiment to XCMSnExp with
as(object, "XCMSnExp").estimatePrecursorIntensity() to a method and add an implementation
for MsExperiment objects.plotPrecursorIons() function.dropFeatureDefinitions() that was not correctly removing additional
metadata from gap-filled chromatographic peaks.rtimeDifferenceThreshold to ObiwarpParam allowing to
customize the threshold used by obiwarp to determine whether gaps are
present in the sequence of retention times of a sample. This addresses/fixes
issue #739.LamaParama class and method for the adjustRtime()
function. Allowing alignment of a dataset based on landmarks (lamas) from an
external reference dataset.matchLamasChromPeaks(),
summarizeMatchLama() and plot(LamaParama) which allows for evaluation of
matching between lamas and chromPeaks.filterFeatures,PercentMissingFilter..empty_chrom_peaks function so an sn column is
returned. Fixes extracting and plotting of peaks after using
manualChromPeaksfilterFeatures function with filter parameters:
RsdFilter, DratioFilter, PercentMissingFilter, BlankFlag. They can be
used ot filter features from XcmsResult and SummarizedExperiment objects.filterSpectra from MsExperiment.breaks_ppm from MsCoreUtils.featureArea function to consider all chromatographic peaks per
feature, not only the one with the highest intensity. As a consequence,
returned m/z and rt ranges might be higher which has an influence in
featureChromatograms, EIC-based feature grouping and, to a lesser extent
also in gap-filling. Related documentation was updated.featureArea function (and related of the
PeakAreaParam-based gap filling).ppm to PeakDensityParam to enable peak-density-based
correspondence throgh m/z-dependent bins along the m/z.chromatogram call for XcmsExperiment objects.XcmsExperiment with negative indices.data in the vignette to faahko.Chromatogram objects extracted from xcms
results: ensure MS level in chromPeaksMatrix is integer.filterMsLevel method for MsExperiment and XcmsExperiment.verboseBetaColumns to CentWaveParam to enable calculation
of additional peak quality metrics comparing the EIC to an idealized bell
curve.param = to generic function storeResults: PlainTextParam to save
an XcmsExperiment or MsExperiment object as colleciton of plain text
files.storeResults and one of its param =: RDataParam to save an
XcmsExperiment object as an .RData file.XcmsExperiment to a xcmsSet (issue #696).mz or rt also for chromatogram,MsExperiment.mz or rt need to be provided for chromatogram.chromPeakChromatograms function to extract (EIC) chromatograms for
chromatographic peaks.isolationWindowTargetMz to the chromatogram function for
MsExperiment and XcmsExperiment to ensure MS2 chromatographic data is
extracted from the MS2 spectra containing fragments of the compound of
interest.xmse data set representing an XcmsExperiment object.loadXcmsData to load test data objects (and fix/update paths).groupFeatures methods for XcmsExperiment.featureArea for XcmsExperiment.findChromPeaksIsolationWindow method for MsExperiment and
XcmsExperiment.reconstructChromPeakSpectra a method.reconstructChromPeakSpectra implementation for XcmsExperiment.filterIsolationWindow for MsExperiment and XcmsExperiment to filter
spectra (and eventually chromatographic peaks) based on the isolation window.featureSummary and overlappingFeatures gain support for XcmsExperiment.featureChromatograms to ensure a valid object is returned.XcmsExperiment and support for MsExperiment/Spectra: add all
functionality for a full xcms processing on a MsExperiment object.refineChromPeaks with MergeNeighboringPeaksParam where a
wrong apex position was considered in the evaluation whether candidate peaks
should be merged (would only happen for merging of > 2 candidate peaks).reconstructChromPeakSpectra for DIA data analysis to fix an
issue with chromatographic peaks in overlapping SWATH isolation windows and
generally to improve performance.chromatogram after filtering a result object (issue #511).fillChromPeaks on sparse data (many empty spectra) and peak
detection performed with MatchedFilterParam (issue #653).rgl package (issue #654).firstBaselineCheck parameter of
centWave.filterFile and similar functions.expandMz to featureChromatograms
https://github.com/sneumann/xcms/issues/612.transformIntensity method.chromPeakSpectra or featureSpectra on an object
that contains also files with only MS1 spectra
(https://github.com/sneumann/xcms/issues/603).plot with type = "XIC" to plot an empty plot if no data is present.manualFeatures allowing to manually define and add features to an
XCMSnExp object.plotChromatogramsOverlay function to support plotting of multiple EICs
from the same sample into the same plot (eventually stacked).EicSimilarityParam.compareChromatograms from MSnbase.AbundanceSimilarityParam.MsFeatures.featureArea function to extract the m/z-rt region for features.featureSpectra function.filterChromPeaks method to filter chromatographic peaks in a
XChromatogram or XChromatograms object.filterChromPeaks method for XCMSnExp (issue #541).Spectra objects by chromPeakSpectra, featureSpectra
and reconstructChromPeakSpectra.chromPeakSpectra.chromPeakSpectra.peaks and features parameter in chromPeakSpectra and
featureSpectra, respectively.Param object from ProtGenerics.filterIntensity, normalize and alignRt for Chromatogram and
MChromatograms from MSnbase.align,Chromatogram gains new method "none" which will only keep values
with identical retention times. For method = "matchRtime" the (much faster)
matching function closest from the MsCoreUtils package is used.correlate,Chromatogram gains parameter useIntensitiesAbove to
perform the correlation only with values larger than this threshold
(avoiding thus high correlation because of many 0-values).filterIntensity,Chromatogram that allows to filter a chromatogram
object keeping only data points with an intensity above a user provided
threshold.manualChromPeaks allowing to manually add and integrate
chromatographic peaks.XChromatograms with drop = FALSE.FilterIntensityParam to filter chromatographic peaks on intensity
(issue #502).estimatePrecursorIntensity function to determine the precursor intensity
for MS2 spectra from the neighboring MS1 spectra.Spectra and Chromatograms to MSpectra and MChromatograms
from MSnbase version >= 2.15.3.reconstructChromPeakSpectra: report also polarity and precusorIntensity.reconstructChromPeakSpectra: ensure a retention time is reported for
reconstructed MS2 spectra (issue #485).expandRt to 0 in reconstructChromPeakSpectra.refineChromPeaks,MergeNeighboringPeaksParam if no peaks found
to be merged.fillChromPeaks,ChromPeakAreaParam to base the area from which missing
peak data should be filled-in on the actually detected chromatographic peaks
of a feature.XCMSnExp to xcmsSet looses phenodata
(thanks to Andris Jankevics for reporting and providing a solution).normalize method for Chromatogram and Chromatograms objects.featureChromatograms gets new parameter n and value to extract EICs
only from the top n samples with highest intensities.filterFile gets new parameter keepFeatures to support retaining
correspondence results even if a data set is filtered by file.Param class.extendLengthMSW in CentWaveParam.
Thanks to William Kumler for contributing the fix.fillChromPeaks.add to allow several rounds of peak detections
on the same object.imputeRowMinRand.mzd in LC-MS/MS vignette.xcmsRaw that leads to a netCDF error message (issue #363).NA.For more details and all changes before May 2012 please see the (now discontinued) CHANGELOG in the source package (inst/ folder).
Other Changes since Version 1.32:
Other Changes since Version 1.14:
New method for grouping: an algorithm inspired by mzMine group(method="nearest") has been implemented. It is slower than group(method="density"). It can individually group close-eluting peaks of very similar mass
New method for retention time correction: The retcor(method="obiwarp") algorithm operates on the raw data, and thus allows to correct runs without well-behaving peak groups, or without peak picking at all.
fillPeaks(method="MSW") is now also available for direct infusion spectra. The findPeaks(method="MSW") now returns several intensities, and correctly reports mzmin and mzmax for peaks.
centWave now uses dynamic memory allocation, needs much less memory, and these BUF related errors should be a thing of the past.
centWave gains an optional argument "noise", which is useful for data that was centroided without any intensity threshold, centroids with intensity < "noise" are omitted from ROI detection
the fillPeaks() methods now remember which was an observed, and which was a "filled" peak.
For direct infusion spectra diffreport() now shows the raw peak shapes, and also indicated "real" and "filled" peaks.
xcmsRaw can now filter for positive/negative spectra, if the file includes both polarities. xcmsSet() can pass the polarity to contain positive/negative peaks only.